An on-line screening method to analyse volatile organic compounds (VOCs) in faecal samples was developed. VOCs were isolated from a standard solution or faecal samples using a purge-and-trap system and identified and quantified by GC-MS. The experimental conditions were optimised and the performance of the system was evaluated. Linear calibration curves were obtained with correlation coefficients of at least 0.992. RSDs within and between days were less than 10%. The method was successfully applied to the analysis of faecal samples, yielding 135 different volatile organic compounds identified in 11 faecal samples. Of those, 22 VOCs were found in all volunteers, whereas 34 VOCs were person-specific.